I see, thanks. It looks like there's something else going on, as I've
looked at the reaction I'm meant to be encoding here, and the intention is
to have a 'wildcard' atom attached to the mapped carbon on the reactant to
make it a CH2-* type environment. Clearly that's not happening, but that's
on
Unless you can make your reactant definitions a lot more specific, I think
you're going to have to do the post-processing.
The RDKit just uses all possible substructure matches of the reactant
templates you provide... it makes no attempt to determine which is "best".
-greg
On Sun, Dec 5, 2021
Hi,
I think there is an issue on the level of your reaction SMARTS, in fact i
cannot get it to work on your example molecules, as there is a methyl
[CH3:0] amine defined in the query which is not to be found in the
substrate. I imagine some more explicit mapping of what connects and what
breaks
Here's the specific example that I was referring to:
I used a reaction with this SMILES, making a ChemicalReaction out of it
using the add reactant templates:
[image: image.png]
N[CH3:1].O=C(O)C(c1c1)C11>>O=C(N[CH3:1])C(c1c1)C11
Taking two reagents to fit it:
[image: image.png]
Hi James,
I am not quite sure I understand what you have done and what you'd like to
achieve.
Ideally, could you please post:
* the reaction you are using
* some example reactants
* the desired product(s)
* the undesired product(s)
Thanks, cheers
p.
On Thu, Dec 2, 2021 at 6:03 PM James Wallace
Hi,
I've been working with the EnumerateLibraryFromReaction function to
generate some quick access molecule libraries, using standard lists of
reagents.
However, when I get the output back, I notice that I get results that chop
up the reactants I use wherever they match the reaction rule, so for
6 matches
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